Fine-Mapping of a Red-Skinned Taproot Gene in Radish (Raphanus sativus L.)

TL;DR

This study identifies a gene responsible for red skin color in radish taproots and its role in anthocyanin synthesis.

Contribution

The study fine-maps a major gene, RST1, and identifies candidate genes involved in anthocyanin synthesis in radish.

Findings

RST1 is a major locus controlling red taproot skin color in radish.

A MYB gene is a candidate for RST1, with RsbHLH and RsWD as potential interacting genes.

RsDFR and RsANS are proposed as target genes of RST1 in the anthocyanin pathway.

Abstract

The skin color of radish taproots is an important commodity character that directly affects the choice behavior of consumers. Here, we identified a skin color gene carried by a red-skinned inbred line, SXAU-R2. Genetic population was constructed by the crossing of SXAU-R2 and a white-skinned inbred line, SXAU-W2, and the taproots of F1 plants exhibited intermediate color. In the F2 population, the separation ratio of taproot skin color indicated that the phenotype was controlled by one major locus, named RST1 (Red-Skinned Taproot 1). Combined with bulked segregant analysis and RNA sequencing (BSA-seq), 2640 single nucleotide polymorphisms (SNPs) were detected between the annotated genes of the red skin bulk and white skin bulk. Molecular markers were developed in the SNP-enriched 27~32 Mbp region of chromosome 7, and then RST1 was mapped in the genetic interval between flanking markers SSR-14 and SSR-22. Using F2:3 lines derived from a key F2 heterozygote, RST1 was narrowed down into a 530 Kbp interval. There were 46 expressed annotated genes in the fine-mapping region, and a gene encoding MYB was selected as the candidate of RST1. Finally, based on Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis and RT-qPCR, we identified the potential interacting genes RsbHLH and RsWD, as well as the latent target genes RsDFR and RsANS of RST1 in the anthocyanin synthesis pathway. These results provide an understanding of the genetic mechanisms regulating anthocyanin synthesis and offer an efficient molecular marker for the radish breeding of skin color.

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